bacteria

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS

🔬🐛 Rapid 16s rRNA identification from isolate FASTQ files

An ensemble of plasmid classification tools

Nanopore sequencing experimental protocols and computational pipelines

Reproducible RNA-seq pipeline for bacterial transcriptomics

WIP & POC: Count Viral and other non-human genome signatures in Human NGS data

Identifying pathogenic bacteria

Curated mirror of RefSeq Microbial Genomes. Available via CVMFS repository.

example genomics workflow for student training

Montagem de genoma bacteriano: Trimmomatic, SPAdes, QUAST, Prokka, BLAST

A simple bacterial variant analysis workflow using FastQC, BWA, samtools and bcftools

MongoDB scripts and data

A structured collection of transcriptomics pipelines for bulk RNA-seq, single-cell, and spatial analysis across bacteria, plants, fungi, and mammals.